LAMMPS (18 Feb 2013)
# 2d LJ obstacle flow

dimension	2
boundary	p s p

atom_style	atomic
neighbor	0.3 bin
neigh_modify	delay 5

# create geometry

lattice		hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region		box block 0 40 0 10 -0.25 0.25
create_box	3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 840 atoms

mass		1 1.0
mass		2 1.0
mass		3 1.0

# LJ potentials

pair_style	lj/cut 1.12246
pair_coeff	* * 1.0 1.0 1.12246

# define groups

region	        1 block INF INF INF 1.25 INF INF
group		lower region 1
120 atoms in group lower
region		2 block INF INF 8.75 INF INF INF
group		upper region 2
120 atoms in group upper
group		boundary union lower upper
240 atoms in group boundary
group		flow subtract all boundary
600 atoms in group flow

set		group lower type 2
  120 settings made for type
set		group upper type 3
  120 settings made for type

# initial velocities

compute	        mobile flow temp
velocity	flow create 1.0 482748 temp mobile
fix		1 all nve
fix		2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify	2 temp mobile

# Poiselle flow

velocity	boundary set 0.0 0.0 0.0
fix		3 lower setforce 0.0 0.0 0.0
fix		4 upper setforce 0.0 NULL 0.0
fix		5 upper aveforce 0.0 -0.5 0.0
fix		6 flow addforce 1.0 0.0 0.0

# 2 obstacles

region		void1 sphere 10 4 0 3
delete_atoms	region void1
Deleted 36 atoms, new total = 804
region		void2 sphere 20 7 0 3
delete_atoms	region void2
Deleted 35 atoms, new total = 769

fix		7 flow indent 100 sphere 10 4 0 4
fix		8 flow indent 100 sphere 20 7 0 4
fix		9 all enforce2d

# Run

timestep	0.003
thermo		1000
thermo_modify	temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)

#dump		1 all atom 100 dump.obstacle

#dump		1 all image 500 image.*.jpg type type #		zoom 1.6 adiam 1.5
#dump_modify	1 pad 5

run		25000
Memory usage per processor = 2.07044 Mbytes
Step Temp E_pair E_mol TotEng Press Volume 
       0    1.0027471            0            0   0.68849216   0.46317653    1143.0857 
    1000            1  -0.33689286            0   0.34971312    1.2905426    1286.7728 
    2000            1  -0.36746164            0   0.31914434    1.1668828      1313.44 
    3000            1  -0.52004751            0   0.16655848    1.4177739     1324.489 
    4000            1  -0.50683869            0   0.17976729    1.4851498     1370.896 
    5000            1  -0.49074513            0   0.19586085    1.2870129    1411.5513 
    6000            1  -0.45051896            0   0.23608702    1.2173953    1441.7581 
    7000            1  -0.44428914            0   0.24231685    1.2136189    1451.7268 
    8000            1  -0.41943736            0   0.26716862    1.0476856    1463.0805 
    9000            1  -0.42143857            0   0.26516741    1.1040812    1449.7584 
   10000            1  -0.40181705            0   0.28478893   0.97148485    1448.5974 
   11000            1   -0.4088962            0   0.27770978    1.1761219    1440.3567 
   12000            1  -0.38630717            0   0.30029881    1.0593811    1444.9934 
   13000            1  -0.37152911            0   0.31507687   0.98075952    1448.0726 
   14000            1  -0.37370096            0   0.31290502    1.0046443    1449.4749 
   15000            1  -0.39915937            0   0.28744662    1.0240313    1452.3583 
   16000            1  -0.37562636            0   0.31097963    1.0053468    1452.3514 
   17000            1  -0.35736161            0   0.32924437     1.070682     1452.898 
   18000            1  -0.38767402            0   0.29893196    1.0418661    1456.1288 
   19000            1  -0.38489181            0   0.30171417    1.0361798    1446.8804 
   20000            1  -0.39521864            0   0.29138735    1.0754044    1447.4619 
   21000            1  -0.37845983            0   0.30814615    1.0072922    1453.8721 
   22000            1  -0.40926684            0   0.27733914    1.0929362    1452.8181 
   23000            1   -0.3586683            0   0.32793768     1.006092    1459.6104 
   24000            1  -0.38908821            0   0.29751777   0.95291948    1464.8522 
   25000            1  -0.38890426            0   0.29770172   0.95284427    1455.9361 
Loop time of 1.73023 on 1 procs for 25000 steps with 769 atoms

Pair  time (%) = 0.509133 (29.4258)
Neigh time (%) = 0.144696 (8.36287)
Comm  time (%) = 0.02689 (1.55413)
Outpt time (%) = 0.000263929 (0.015254)
Other time (%) = 1.04924 (60.6419)

Nlocal:    769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    1624 ave 1624 max 1624 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1624
Ave neighs/atom = 2.11183
Neighbor list builds = 1642
Dangerous builds = 0
